chr6-3338872-C-T

Variant names:

• chr6-3338872-C-T
• rs7747259
• NM_015482.2:c.914-14870G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015482.2(SLC22A23):​c.914-14870G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,112 control chromosomes in the GnomAD database, including 5,884 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (5884 hom., cov: 33)
• Consequence: SLC22A23 NM_015482.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341
• Publications: 1 publications found

Genes affected

SLC22A23 (HGNC:21106): (solute carrier family 22 member 23) SLC22A23 belongs to a large family of transmembrane proteins that function as uniporters, symporters, and antiporters to transport organic ions across cell membranes (Jacobsson et al., 2007 [PubMed 17714910]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015482.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A23	NM_015482.2	MANE Select	c.914-14870G>A		intron	N/A	NP_056297.1
	SLC22A23	NM_001382317.1		c.914-14870G>A		intron	N/A	NP_001369246.1
	SLC22A23	NM_001286455.1		c.71-14870G>A		intron	N/A	NP_001273384.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A23	ENST00000406686.8	TSL:5 MANE Select	c.914-14870G>A		intron	N/A	ENSP00000385028.3
	SLC22A23	ENST00000485307.5	TSL:1	c.398-14870G>A		intron	N/A	ENSP00000418134.1
	SLC22A23	ENST00000380302.8	TSL:1	c.71-14870G>A		intron	N/A	ENSP00000369657.4

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36990 AN: 151994 Hom.: 5863 Cov.: 33

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.241

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.244 AC: 37060 AN: 152112 Hom.: 5884 Cov.: 33 AF XY: 0.238 AC XY: 17741 AN XY: 74392

African (AFR) AF: 0.446 AC: 18472 AN: 41432

American (AMR) AF: 0.165 AC: 2525 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3468

East Asian (EAS) AF: 0.228 AC: 1181 AN: 5178

South Asian (SAS) AF: 0.266 AC: 1284 AN: 4826

European-Finnish (FIN) AF: 0.0587 AC: 622 AN: 10602

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11516 AN: 67988

Other (OTH) AF: 0.239 AC: 505 AN: 2114

Alfa AF: 0.203 Hom.: 663

Bravo AF: 0.260

Asia WGS AF: 0.236 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.22
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7747259; hg19: chr6-3339106;